12/4/12
Dr. Sanjeeva Srivastava IIT Bombay •  Proteins and its function
•  Amino acids: building blocks
•  Different levels of protein structure
•  Primary, Secondary, Tertiary, Quaternary
IIT Bombay
2 Proteomics Course
NPTEL
1
12/4/12
•  Derived from Greek “Proteios”
•  Linear polymers built of monomers (amino
acids)
•  Most versatile macromolecules in living systems
•  Play key structural and functional roles
3 Proteomics Course
Message Promoter IIT Bombay
NPTEL
T A T A C A Q G T A C Y C G T R Protein Sequence & Regula5on Protein Structure Protein/ Enzyme Structure DNA Sequence IIT Bombay
4 Proteomics Course
NPTEL
2
12/4/12
Off SIGNALLING On TRANSPORT REGULATION Protein Functions STRUCTURE CATALYSIS Α
MOVEMENT Β IIT Bombay
5 Proteomics Course
NPTEL
IIT Bombay
6 Proteomics Course
NPTEL
3
12/4/12
-­‐ COO COO -­‐ -­‐ COO + +
H N C H H 3 N C H H CH3 3
Glycine +
H 2 N H
C CH 3 +
H 3 N C H CH2OH Serine -­‐ COO + H 3 N C H CH2 CH 3 Isoleucine Methionine O Asparagine 8 NPTEL
-­‐ COO -­‐ COO + +
H 3 N C H H N C H H C OH CH2 3
CH3 SH Threonine Cysteine -­‐ COO + H 3 N C H CH2 CH2 C IIT Bombay
S CH3 Proteomics Course
-­‐ COO H2 N Valine CH2 7 IIT Bombay
CH 3 CH2 CH2 Leucine CH 3 + CH2 CH 3 CH CH2 H 3 N C H H 3 N C H CH 3 CH2 -­‐ COO +
H 3 N C H CH +
H 3 N C H Proline -­‐ COO + H C H2C Alanine -­‐ COO -­‐ COO C H2 N O Glutamine Proteomics Course
NPTEL
4
12/4/12
-­‐ COO +
-­‐ COO H 3 N C H H 3 N C H CH2 CH2 CH2 CH2 CH2 CH2 CH 2 NH + NH3 C NH2 9 CH2 C + H 3 N C H CH + NH2 His5dine NPTEL
-­‐ COO +
H 3 N C H CH2 CH2 -­‐ COO CH2 -­‐ COO Glutamate Aspartate 10 NH C N H Proteomics Course
-­‐ COO IIT Bombay
+ H 3 N C H Arginine Lysine IIT Bombay
-­‐ COO + Proteomics Course
NPTEL
5
12/4/12
-­‐ COO -­‐ COO -­‐ COO +
H 3 N C H + H 3 N C H +
H 3 N C H CH2 CH2 C CH2 CH NH OH Phenylalanine Tyrosine Tryptophan Hydrophobic character
Hydrophobic
IIT Bombay
11 Hydrophilic
Proteomics Course
NPTEL
Extinction coefficient
10,000 8,000 6,000 4,000 2,000 0 220 240 260 280 300 320 Wavelength (nm)
IIT Bombay
12 Proteomics Course
NPTEL
6
12/4/12
D-­‐Isomer L-­‐Isomer  
 Cα NH3 H
Cα COO‫ ־‬ COO‫ ־‬ 


IIT Bombay
 R
R
H
13 NH3 
Proteomics Course
NPTEL

R
 H
Cα NH3 COO‫ ־‬ 

IIT Bombay
14 Proteomics Course
NPTEL
7
12/4/12
R H
R H
C
C
C
+ H N
3
R H
+ H N
3
+ H N
3
Zwitterionic Form
Both groups
Protonated
Both groups
Protonated
0 2 4 6 8 10 12 14 IIT Bombay
15 Proteomics Course
NPTEL
R2 R1 +
C C R1 H C O IIT Bombay
16 C H C +H3N C N C H N N
+
Proteomics Course
+ H20 R2 NPTEL
8
12/4/12
R1 H C N C H O H O N C C R2 H R3 H C N C H O H O N C C R4 H Backbone IIT Bombay
17 Proteomics Course
NPTEL
H Cα N Cα C O IIT Bombay
18 Proteomics Course
NPTEL
9
12/4/12
H C H N C N +
C C C O IIT Bombay
C O¯ˉ 19 Proteomics Course
NPTEL
Trans Trans H Cα N C Cα O O
C Cα IIT Bombay
20 Proteomics Course
H
Cis N
Cα NPTEL
10
12/4/12
Cis O
C Cα N
Cα H N
Cα Cα C O
Trans IIT Bombay
21 Proteomics Course
NPTEL
IIT Bombay
22 Proteomics Course
NPTEL
11
12/4/12
Alanine Glycine 4H2O Condensa5on Valine Lysine Primary Structure Free amino acids 23 IIT Bombay
Proteomics Course
NPTEL
OH CH3 CH3 HC H2C H C O N C C +H3N O IIT Bombay
H 24 C H H H H H C O N N C H O Proteomics Course
N H H C C C H2C H2C C _ H NPTEL
12
12/4/12
•  Essential for elucidation of its mechanism of action
•  Determines 3-D structure of proteins
•  Amino acid alteration can produce abnormality
•  Sequence tells us an evolutionary history of protein
IIT Bombay
25 Proteomics Course
NPTEL
R2 H Cα H H Cα N Ψ C H O R1 IIT Bombay
N H C Cα R3 26 Proteomics Course
NPTEL
13
Phi Ψ -­‐180 -­‐150 -­‐120 -­‐90 -­‐60 -­‐30 0 30 60 90 120 150 180 12/4/12
-­‐180 -­‐150 -­‐120 -­‐90 -­‐60 -­‐30 0 30 60 90 120 150 180 Psi = 90°, Ψ = - 90° IIT Bombay
27 Proteomics Course
NPTEL
IIT Bombay
28 Proteomics Course
NPTEL
14
12/4/12
Ball and stick model
29 IIT Bombay
Ri
Proteomics Course
H H C Ribbon diagram
N C H O N O C Ri+1 H C Ri+2 H C NPTEL
H N C H O N O C C Ri+3 H Ri+4
H C H N C H O N O C C Ri+5 H Residue i (CO) ____________i + 4 (NH)
IIT Bombay
30 Proteomics Course
NPTEL
15
12/4/12
•  α-Keratin
•  Two α helices wrap to form a stable structure
•  Collagen
•  It contains 3 helical polypeptide chain
IIT Bombay
31 Proteomics Course
NPTEL
•  β sheets: another common, periodic structural
motif
•  Fully extended structure
•  Parallel
•  Anti-parallel
IIT Bombay
32 Proteomics Course
NPTEL
16
12/4/12
•  More elaborate structures loops or omega turns
•  Loops are rigid, no periodic structures
•  Turns and loops on surfaces
•  Participate in protein and other molecule
interactions
IIT Bombay
33 Proteomics Course
α helix
NPTEL
β sheets
Polypeptide chain tightly
coiled
Polypeptide chain fully
extended
Rod like structure
Sheet like structure
Axial distance 1.5 A
Axial distance 3.5 A
H-bond between NH and CO
groups in same polypeptide
chains
H-bond between NH and CO
groups in different polypeptide
chains
Examples – Ferritin, keratin,
collagen
Fatty acid binding protein
IIT Bombay
34 Proteomics Course
NPTEL
17
12/4/12
IIT Bombay
35 Proteomics Course
NPTEL
•  Three dimensional compactly folded structure
of proteins
•  Overall organization of secondary structural
elements in 3-D space
IIT Bombay
36 Proteomics Course
NPTEL
18
12/4/12
IIT Bombay
37 Proteomics Course
NPTEL
•  Final level of protein structure
•  Spatial arrangement of subunits and their
interactions
•  Polypeptide chains assemble to form multisubunit
structure
IIT Bombay
38 Proteomics Course
NPTEL
19
12/4/12
α- subunits
α
β
β
α
Individual polypeptide chains
β- subunits
Quaternary structure
(Hemoglobin)
IIT Bombay
39 DNA
Genetic
blueprint
IIT Bombay
40 Proteomics Course
RNA
molecular
photocopy
Proteomics Course
NPTEL
Proteins
Building
blocks
NPTEL
20
12/4/12
•  Proteins and its function
•  Amino acids: building blocks
•  Different levels of protein structure
•  Primary, Secondary, Tertiary, Quaternary
•  Myoglobin and Hemoglobin
•  Proteins and diseases
IIT Bombay
41 Proteomics Course
NPTEL
•  Berg J., Tmyoczko J. & Stryer L., Biochemitry fifth ed., W. H.
Freeman & company, 2002. ISBN: 0716746840.
•  Nelson D. & Cox M.,Lehninger, Principles of Biochemistry
fourth ed., W. H. Freeman and company, 2004. . ISBN:
023022699X.
•  Voet D. & Voet J., Biochemistry fourth ed., Wiley, 2000.
ISBN: 047158651X.
IIT Bombay
Proteomics Course
NPTEL
21